Pigment Assembly Research Articles

Genome-wide identification and expression profiling of photosystem II (PsbX) gene family in upland cotton (Gossypium hirsutum L)

BackgroundPhotosystem II (PSII) constitutes an intricate assembly of protein pigments, featuring extrinsic and intrinsic polypeptides within the photosynthetic membrane. The low-molecular-weight transmembrane protein PsbX has been identified in PSII, which is associated with the oxygen-evolving complex. The expression of PsbX gene protein is regulated by light. PsbX's central role involves the regulation of PSII, facilitating the binding of quinone molecules to the Qb (PsbA) site, and it additionally plays a crucial role in optimizing the efficiency of photosynthesis. Despite these insights, a comprehensive understanding of the PsbX gene's functions has remained elusive.ResultsIn this study, we identified ten PsbX genes in Gossypium hirsutum L. The phylogenetic analysis results showed that 40 genes from nine species were classified into one clade. The resulting sequence logos exhibited substantial conservation across the N and C terminals at multiple sites among all Gossypium species. Furthermore, the orthologous/paralogous, Ka/Ks ratio revealed that cotton PsbX genes subjected to positive as well as purifying selection pressure might lead to limited divergence, which resulted in the whole genome and segmental duplication. The expression patterns of GhPsbX genes exhibited variations across specific tissues, as indicated by the analysis. Moreover, the expression of GhPsbX genes could potentially be regulated in response to salt, intense light, and drought stresses. Therefore, GhPsbX genes may play a significant role in the modulation of photosynthesis under adverse abiotic conditions.ConclusionWe examined the structure and function of PsbX gene family very first by using comparative genomics and systems biology approaches in cotton. It seems that PsbX gene family plays a vital role during the growth and development of cotton under stress conditions. Collectively, the results of this study provide basic information to unveil the molecular and physiological function of PsbX genes of cotton plants.

Experimental and Theoretical Mutation of Exciton States on the Smallest Type-I Photosynthetic Reaction Center Complex of a Green Sulfur Bacterium Chlorobaclum tepidum.

The exciton states on the smallest type-I photosynthetic reaction center complex of a green sulfur bacterium Chlorobaculum tepidum (GsbRC) consisting of 26 bacteriochlorophylls a (BChl a) and four chlorophylls a (Chl a) located on the homodimer of two PscA reaction center polypeptides were investigated. This analysis involved the study of exciton states through a combination of theoretical modeling and the genetic removal of BChl a pigments at eight sites. (1) A theoretical model of the pigment assembly exciton state on GsbRC was constructed using Poisson TrESP (P-TrESP) and charge density coupling (CDC) methods based on structural information. The model reproduced the experimentally obtained absorption spectrum, circular dichroism spectrum, and excitation transfer dynamics, as well as explained the effects of mutation. (2) Eight BChl a molecules at different locations on the GsbRC were selectively removed by genetic exchange of the His residue, which ligates the central Mg atom of BChl a, with the Leu residue on either one or two PscAs in the RC. His locations are conserved among all type-I RC plant polypeptide, cyanobacteria, and bacteria amino acid sequences. (3) Purified mutant-GsbRCs demonstrated distinct absorption and fluorescence spectra at 77 K, which were different from each other, suggesting successful pigment removal. (4) The same mutations were applied to the constructed theoretical model to analyze the outcomes of these mutations. (5) The combination of theoretical predictions and experimental mutations based on structural information is a new tool for studying the function and evolution of photosynthetic reaction centers.

Theoretical Study on Photothermal Properties of Azobenzene Sulfonate/Magnesium-Aluminum Hydroxide Composite Dye.

The assembly of various azo dyes and pigments with inorganic layered materials could develop new types of intercalation materials. The electronic structures and photothermal properties of composite materials (AbS--LDH) constituted by azobenzene sulfonate anions (AbS-) and Mg-Al layered double hydroxide (LDH) lamella were theoretically studied at the M06-2X/def2-TZVP//M06-2X/6-31G(d,p) level using density functional theory and time-dependent density functional theory. Meanwhile, the influences of LDH lamella on the AbS- in AbS--LDH materials were investigated. The calculated results showed that the addition of LDH lamella could lower the isomerization energy barrier of CAbS- anions (CAbS- stands for cis AbS-). The thermal isomerization mechanisms of AbS--LDH and AbS were related to the conformational change of the azo group, out-of-plane rotation and in-plane inversion. The LDH lamella could reduce the energy gap of the n → π* and π → π* electronic transition and lead to a red-shift in the absorption spectra. When a polar solvent DMSO was applied, the excitation energy of the AbS--LDHs was increased, making its photostability stronger than in nonpolar solvent and solvent-free.

Unravelling the Role of Water in Ultrafast Excited-State Relaxation Dynamics within Nano-Architectures of Chlorophyll a.

Water plays a pivotal role in structural stability of supramolecular pigment assemblies designed for natural light harvesting (for example, chlorosome antenna complex) as well as their artificial analogs. However, the dynamic role of water in the context of excite-state relaxation has not been explored till date, which we report here. Using femtosecond transient absorption spectroscopy, we investigate the excited-state dynamics of two types of nano-scale assemblies of chlorophyll a with different structural motifs, rod-shaped and micellar assemblies, that depend on the water content. We show how water participates in excess energy dissipation by vibrational cooling of the non-thermally populated Qy band at different rates in different types of clusters but exhibits no polar solvation dynamics. For the micelles, we observe a bifurcation of stimulated emission line shape, whereas a positive-to-negative switching of differential absorption is observed for the rods; both these observations are correlated with their specific structural aspects. Density functional theory calculations reveal two possible stable ground state geometries of dimers, accounting for the bifurcation of line shape in micelles. Thus, our study elucidates water-mediated structure-function relationship within these pigment assemblies.

Special issue in honour of Prof. Reto J. Strasser - Effect of AtLFNR1 deficiency on chlorophyll a fluorescence rise kinetics OJIP of Arabidopsis

Leaf-type ferredoxin-NADP(H) oxidoreductase, encoded by AtLFNR1 gene in Arabidopsis, extensively exists in chloroplast stroma and thylakoids and is responsible for the reduction of NADP+ to NADPH in PSI. To investigate the relationship between the characteristics of chlorophyll a fluorescence transients OJIP and the function of AtLFNR1 protein, the fluorescence rise kinetics OJIP curves of AtLFNR1 mutant leaves were determined. It is observed that AtLFNR1 mutant has a lower level of variable fluorescence intensity relative to wild type, especially the J-step and the IP-phase. The JIP-test analysis suggests that the loss of AtLFNR1 function decreases clearly the oxidation rate of plastocyanin as well as PSI reaction center, damages slightly PSII antenna size and pigment assemblies, but stimulates distinctly the photosynthetic activity of PSII. Such multiple effects contribute to the change of shape characteristics of the OJIP transient curve in AtLFNR1 mutant.

Special issue in honour of Prof. Reto J. Strasser - Action of alamethicin in photosystem II probed by the fast chlorophyll fluorescence rise kinetics and the JIP-test

Alamethicin (AMT) is a linear antimicrobial peptide isolated from fungi Trichoderma viride. To date, the mode of action of AMT in plant cells remains unknown. Our experimental results indicate that AMT causes leaf lesion attributed to its multiple effects on PSII. AMT decreases the O2 evolution rate of PSII. Based on chlorophyll fluorescence data, similar to the classical herbicide diuron, AMT interrupts PSII electron transfer beyond QA at the acceptor side, leading to the inactivation of the PSII reaction centers. Additionally, AMT decreases chlorophyll content and destroys the architecture of PSII pigment assemblies. However, AMT does not affect the oxygen-evolving complex at the donor side of PSII. Thus, it is concluded that AMT is a natural photosynthetic inhibitor with several action sites in PSII.

Tuning effect of local environment to control mechanism of fluorescence depolarization: Rotational diffusion and resonance energy transfer within homo-aggregates of xanthenes

Controlling excitation energy transfer within self-assembled molecular aggregates has been a major challenge since such systems represent as prototypes for highly efficient light-harvesting pigment assemblies within photosynthetic organisms. Using time-resolved fluorescence depolarization studies, here we report complete reversal of trends in anisotropy decay traces up on increasing fluorophore concentration while traversing a series of solvent mixtures (water and glycerol) with increasing viscosity. For glycerol, in dilute solution depolarization results from rotational diffusion whereas Förster resonance energy transfer (FRET) is found to be the key mechanism in concentrated solution; in contrast, for water, rotational diffusion is the dominant reason for fluorescence depolarization at all concentrations. We further investigate how viscosity, rather than dielectric constant of the solvent, controls contribution from FRET towards depolarization by partially immobilizing the fluorophores. The results are explained within the framework of analytical models for fluorescence depolarization due to either rotational diffusion or FRET. We further examine the unusual ‘dip-and-rise’ behavior in anisotropy traces for intermediate range of concentration which is suggestive of presence of heterogeneity within homochromophoric system. These results show how one can fine-tune the explicit nature of solvent to facilitate FRET over other competing dynamical processes.

Phagen-codierte metabolische Hilfsgene krempeln den Wirtsstoffwechsel um

Auxiliary metabolic genes (AMGs) are commonly found in the genomes of marine cyanophages and on metagenomic scaffolds originating from phages. Many of them encode proteins involved in photosynthesis and are thought to increase phage fitness during infection. Here, we summarize the biochemical properties of AMG-encoded proteins involved in light harvesting pigment biosynthesis and assembly.

Comparative phytotoxicity of usnic acid, salicylic acid, cinnamic acid and benzoic acid on photosynthetic apparatus of Chlamydomonas reinhardtii

The effects of four phytotoxins usnic acid (UA), salicylic acid (SA), cinnamic acid (CA) and benzoic acid (BA) on photosynthesis of Chlamydomonas reinhardtii were studied in vivo to identify and localise their initial action sites on two photosystems. Our experimental evidence shows that the four phytotoxins have multiple targets in chloroplasts, which mainly lie in photosystem II (PSII), not photosystem I (PSI). They share an original action site by blocking electron transport beyond QA (primary plastoquinone acceptor) at PSII acceptor side since a fast increase of the J-step level is the greatest change in chlorophyll a fluorescence induction kinetics OJIP in C. reinhardtii cells treated with the phytotoxins. UA decreases photosynthetic activity by reducing O2 evolution rate, interrupting PSII electron transport at both the donor and acceptor sides, inactivating the PSII reaction centers (RCs), reducing the content of chlorophylls and carotenoids, destroying the conformation of antenna pigment assemblies, and casuing the degradation of D1/D2 proteins. SA damage to photosynthetic machinery is mainly attributed to inhibition of PSII electron transport beyond QA at the acceptor side, inactivation of the PSII RCs, reduction of chlorophyll content, digestion of thylakoid ploypeptides and destabilization of thylakoid membranes. Both CA and BA affect the photosynthetic process by decreasing PSII electron transport efficiency at the acceptor side and the amount of active PSII RCs. Besides, the initial cause of BA-inhibiting photosynthesis is also assocaited with the O2 evolution rate and the disconnection of some antenna molecules from PSII RCs.

Electronic Absorption Spectra of Tetrapyrrole-Based Pigments via TD-DFT: A Reduced Orbital Space Study.

Tetrapyrrole-based pigments play a crucial role in photosynthesis as principal light absorbers in light-harvesting chemical systems. As such, accurate theoretical descriptions of the electronic absorption spectra of these pigments will aid in the proper description and understanding of the overall photophysics of photosynthesis. In this work, time-dependent density functional theory (TD-DFT) at the CAM-B3LYP/6-31G* level of theory is employed to produce the theoretical absorption spectra of several tetrapyrrole-based pigments. However, the application of TD-DFT to large systems with several hundreds of atoms can become computationally prohibitive. Therefore, in this study, TD-DFT calculations with reduced orbital spaces (ROSs) that exclude portions of occupied and virtual orbitals are pursued as a viable, computationally cost-effective alternative to conventional TD-DFT calculations. The effects of reducing orbital space size on theoretical spectra are qualitatively and quantitatively described, and both conventional and ROS results are benchmarked against experimental absorption spectra of various tetrapyrrole-based pigments. The orbital reduction approach is also applied to a large natural pigment assembly that comprises the principal light-absorbing component of the reaction center in purple bacteria. Overall, we find that TD-DFT calculations with proper and judicious orbital space reductions can adequately reproduce conventional, full orbital space, TD-DFT results of all pigments studied in this work.

Chlorosome-Inspired Synthesis of Templated Metallochlorin-Lipid Nanoassemblies for Biomedical Applications.

Chlorosomes are vesicular light-harvesting organelles found in photosynthetic green sulfur bacteria. These organisms thrive in low photon flux environments due to the most efficient light-to-chemical energy conversion, promoted by a protein-less assembly of chlorin pigments. These assemblies possess collective absorption properties and can be adapted for contrast-enhanced bioimaging applications, where maximized light absorption in the near-infrared optical window is desired. Here, we report a strategy for tuning light absorption toward the near-infrared region by engineering a chlorosome-inspired assembly of synthetic metallochlorins in a biocompatible lipid scaffold. In a series of synthesized chlorin analogues, we discovered that lipid conjugation, central coordination of a zinc metal into the chlorin ring, and a 3(1)-methoxy substitution were critical for the formation of dye assemblies in lipid nanovesicles. The substitutions result in a specific optical shift, characterized by a bathochromically shifted (72 nm) Qy absorption band, along with an increase in absorbance and circular dichroism as the ratio of dye-conjugated lipid was increased. These alterations in optical spectra are indicative of the formation of delocalized excitons states across each molecular assembly. This strategy of tuning absorption by mimicking the structures found in photosynthetic organisms may spur new opportunities in the development of biophotonic contrast agents for medical applications.

Role of Lipids in Chloroplast Biogenesis.

Chloroplasts are plant organelles that develop the thylakoid membrane inside to perform oxygenic photosynthesis. The biogenesis of the thylakoid membrane requires coordinated synthesis and assembly of proteins, pigments and many photosynthetic cofactors with membrane glycerolipids. The lipid bilayer of the thylakoid membrane mainly consists of four lipid classes; monogalactosyldiacylglycerol (MGDG), digalactosyldiacylglycerol (DGDG), sulfoquinovosyldiacylglycerol (SQDG) and phosphatidylglycerol (PG), each of which has specific roles in biogenesis and maintenance of thylakoid membranes and photosynthesis. Galactolipids MGDG and DGDG constitute the bulk of membrane lipids in chloroplasts and are essential as major structural components of the thylakoid membrane. In addition to galactolipids, the thylakoid membrane requires a certain level of anionic lipids SQDG and PG for its function. Although SQDG and PG substitute for each other to maintain the amount of total anionic lipids in chloroplasts, PG has specific roles in photosynthesis that cannot be compensated by SQDG and galactolipids. In this chapter, we summarize roles of lipids in chloroplast functions with their biosynthetic pathways, which have been mainly established in Arabidopsis, and discuss an involvement of lipid biosynthesis in coordinated development of photosynthetic machinery during chloroplast biogenesis.

Roles of Tetratricopeptide Repeat Proteins in Biogenesis of the Photosynthetic Apparatus.

Biosynthesis of the photosynthetic apparatus is a complex operation, which includes the concerted synthesis and assembly of lipids, pigments and metal cofactors, and dozens of proteins. Research conducted in recent years has shown that these processes, as well as the stabilization and repair of this molecular machinery, are facilitated by transiently acting regulatory proteins, many of which belong to the superfamily of helical repeat proteins. Here, we focus on one of its families in photoautotrophic model organisms, the tetratricopeptide repeat (TPR) proteins, which participate in almost all of these steps and are crucial for biogenesis of the thylakoid membrane.

Photosystem II Assembly Steps Take Place in the Thylakoid Membrane of the Cyanobacterium Synechocystis sp. PCC6803.

Thylakoid biogenesis is an intricate process requiring accurate and timely assembly of proteins, pigments and other cofactors into functional, photosynthetically competent membranes. PSII assembly is studied in particular as its core protein, D1, is very susceptible to photodamage and has a high turnover rate, particularly in high light. PSII assembly is a modular process, with assembly steps proceeding in a specific order. Using aqueous two-phase partitioning to separate plasma membranes (PM) and thylakoid membranes (TM), we studied the subcellular localization of the early assembly steps for PSII biogenesis in a Synechocystis sp. PCC6803 cyanobacterium strain lacking the CP47 antenna. This strain accumulates the early D1-D2 assembly complex which was localized in TM along with associated PSII assembly factors. We also followed insertion and processing of the D1 precursor (pD1) by radioactive pulse-chase labeling. D1 is inserted into the membrane with a C-terminal extension which requires cleavage by a specific protease, the C-terminal processing protease (CtpA), to allow subsequent assembly of the oxygen-evolving complex. pD1 insertion as well as its conversion to mature D1 under various light conditions was seen only in the TM. Epitope-tagged CtpA was also localized in the same membrane, providing further support for the thylakoid location of pD1 processing. However, Vipp1 and PratA, two proteins suggested to be part of the so-called 'thylakoid centers', were found to associate with the PM. Together, these results suggest that early PSII assembly steps occur in TM or specific areas derived from them, with interaction with PM needed for efficient PSII and thylakoid biogenesis.

Mantle Branch-Specific RNA Sequences of Moon Scallop Amusium pleuronectes to Identify Shell Color-Associated Genes.

Amusium pleuronectes (Linnaeus) that secretes red- and white-colored valves in two branches of mantle tissues is an excellent model for shell color research. High-throughput transcriptome sequencing and profiling were applied in this project to reveal the detailed molecular mechanism of this phenotype differentiation. In this study, 50,796,780 and 54,361,178 clean reads were generated from the left branch (secreting red valve, RS) and right branch (secreting white valve, WS) using the Illumina Hiseq 2000 platform. De novo assembly generated 149,375 and 176,652 unigenes with an average length of 764 bp and 698 bp in RS and WS, respectively. Kyoto encyclopedia of genes and genomes (KEGG) metabolic pathway analysis indicated that the differentially expressed genes were involved in 228 signaling pathways, and 43 genes were significantly enriched (P<0.01). Nineteen of 20 differentially expressed vitellogenin genes showed significantly high expression in RS, which suggested that they probably played a crucial role in organic pigment assembly and transportation of the shell. Moreover, 687 crystal formation-related (or biomineralization-related) genes were detected in A. pleuronectes, among which 144 genes exhibited significant difference between the two branches. Those genes could be classified into shell matrix framework participants, crystal nucleation and growth-related elements, upstream regulation factors, Ca level regulators, and other classifications. We also identified putative SNP and SSR markers from these samples which provided the markers for genetic diversity analysis, genetic linkage, QTL analysis. These results provide insight into the complexity of shell color differentiation in A. pleuronectes so as valuable resources for further research.

Circularly polarized luminescence spectroscopy reveals low-energy excited states and dynamic localization of vibronic transitions in CP43

Circularly polarized luminescence (CPL) spectroscopy is an established but relatively little-used technique that monitors the chirality of an emission. When applied to photosynthetic pigment assemblies, we find that CPL provides sensitive and detailed information on low-energy exciton states, reflecting the interactions, site energies and geometries of interacting pigments. CPL is the emission analog of circular dichroism (CD) and thus spectra explore the optical activity only of fluorescent states of the pigment-protein complex and consequently the nature of the lowest-energy excited states (trap states), whose study is a critical area of photosynthesis research. In this work, we develop the new approach of temperature-dependent CPL spectroscopy, over the 2–120K temperature range, and apply it to the CP43 proximal antenna protein of photosystem II. Our results confirm strong excitonic interactions for at least one of the two well-established emitting states of CP43 named “A” and “B”. Previous structure-based models of CP43 spectra are evaluated in the light of the new CPL data. Our analysis supports the assignments of Shibata et al. [Shibata et al. J. Am. Chem. Soc. 135 (2013) 6903–6914], particularly for the highly-delocalized B-state. This state dominates CPL spectra and is attributed predominantly to chlorophyll a's labeled Chl 634 and Chl 636 (alternatively labeled Chl 43 and 45 by Shibata et al.). The absence of any CPL intensity in intramolecular vibrational sidebands associated with the delocalized “B” excited state is attributed to the dynamic localization of intramolecular vibronic transitions.

Ground-State Electronic Structure of RC-LH1 and LH2 Pigment Assemblies of Purple Bacteria via the EBF-MO Method.

Light-harvesting antennas are protein-pigment complexes that play a crucial role in natural photosynthesis. The antenna complexes absorb light and transfer energy to photosynthetic reaction centers where charge separation occurs. This work focuses on computational studies of the electronic structure of the pigment networks of light-harvesting complex I (LH1), LH1 with the reaction center (RC-LH1), and light-harvesting complex II (LH2) found in purple bacteria. As the pigment networks of LH1, RC-LH1, and LH2 contain thousands of atoms, conventional density functional theory (DFT) and ab initio calculations of these systems are not computationally feasible. Therefore, we utilize DFT in conjunction with the energy-based fragmentation with molecular orbitals method and a semiempirical approach employing the extended Hückel model Hamiltonian to determine the electronic properties of these pigment assemblies. Our calculations provide a deeper understanding of the electronic structure of natural light-harvesting complexes, especially their pigment networks, which could assist in rational design of artificial photosynthetic devices.

The proteolysis adaptor, NblA, is essential for degradation of the core pigment of the cyanobacterial light-harvesting complex.

The cyanobacterial light-harvesting complex, the phycobilisome, is degraded under nutrient limitation, allowing the cell to adjust light absorbance to its metabolic capacity. This large light-harvesting antenna comprises a core complex of the pigment allophycocyanin, and rod-shaped pigment assemblies emanating from the core. NblA, a low-molecular-weight protein, is essential for degradation of the phycobilisome. NblA mutants exhibit high absorbance of rod pigments under conditions that generally elicit phycobilisome degradation, implicating NblA in degradation of these pigments. However, the vast abundance of rod pigments and the substantial overlap between the absorbance spectra of rod and core pigments has made it difficult to directly associate NblA with proteolysis of the phycobilisome core. Furthermore, lack of allophycocyanin degradation in an NblA mutant may reflect a requirement for rod degradation preceding core degradation, and does not prove direct involvement of NblA in proteolysis of the core pigment. Therefore, in this study, we used a mutant lacking phycocyanin, the rod pigment of Synechococcus elongatusPCC7942, to examine whether NblA is required for allophycocyanin degradation. We demonstrate that NblA is essential for degradation of the core complex of the phycobilisome. Furthermore, fluorescence lifetime imaging microscopy provided insitu evidence for the interaction of NblA with allophycocyanin, and indicated that NblA interacts with allophycocyanin complexes that are associated with the photosynthetic membranes. Based on these data, as well as previous observations indicating interaction of NblA with phycobilisomes attached to the photosynthetic membranes, we suggest a model for sequential phycobilisome disassembly by NblA.

Solid-state NMR Reveals the Carbon-based Molecular Architecture of Cryptococcus neoformans Fungal Eumelanins in the Cell Wall

Melanin pigments protect against both ionizing radiation and free radicals and have potential soil remediation capabilities. Eumelanins produced by pathogenic Cryptococcus neoformans fungi are virulence factors that render the fungal cells resistant to host defenses and certain antifungal drugs. Because of their insoluble and amorphous characteristics, neither the pigment bonding framework nor the cellular interactions underlying melanization of C. neoformans have yielded to comprehensive molecular-scale investigation. This study used the C. neoformans requirement of exogenous obligatory catecholamine precursors for melanization to produce isotopically enriched pigment "ghosts" and applied 2D (13)C-(13)C correlation solid-state NMR to reveal the carbon-based architecture of intact natural eumelanin assemblies in fungal cells. We demonstrated that the aliphatic moieties of solid C. neoformans melanin ghosts include cell-wall components derived from polysaccharides and/or chitin that are associated proximally with lipid membrane constituents. Prior to development of the mature aromatic fungal pigment, these aliphatic moieties form a chemically resistant framework that could serve as the scaffold for melanin synthesis. The indole-based core aromatic moieties show interconnections that are consistent with proposed melanin structures consisting of stacked planar assemblies, which are associated spatially with the aliphatic scaffold. The pyrrole aromatic carbons of the pigments bind covalently to the aliphatic framework via glycoside or glyceride functional groups. These findings establish that the structure of the pigment assembly changes with time and provide the first biophysical information on the mechanism by which melanin is assembled in the fungal cell wall, offering vital insights that can advance the design of bioinspired conductive nanomaterials and novel therapeutics.

Structure of the LH1–RC complex from Thermochromatium tepidum at 3.0 Å

The light-harvesting core antenna (LH1) and the reaction centre (RC) of purple photosynthetic bacteria form a supramolecular complex (LH1-RC) to use sunlight energy in a highly efficient manner. Here we report the first near-atomic structure, to our knowledge, of a LH1-RC complex, namely that of a Ca(2+)-bound complex from Thermochromatium tepidum, which reveals detailed information on the arrangement and interactions of the protein subunits and the cofactors. The RC is surrounded by 16 heterodimers of the LH1 αβ-subunit that form a completely closed structure. The Ca(2+) ions are located at the periplasmic side of LH1. Thirty-two bacteriochlorophyll and 16 spirilloxanthin molecules in the LH1 ring form an elliptical assembly. The geometries of the pigment assembly involved in the absorption characteristics of the bacteriochlorophyll in LH1 and excitation energy transfer among the pigments are reported. In addition, possible ubiquinone channels in the closed LH1 complex are proposed based on the atomic structure.